Structure-guided design of a reversible fluorogenic reporter of protein-protein interactions

A reversible green fluorogenic protein-fragment complementation assay was developed based on the crystal structure of UnaG, a recently discovered fluorescent protein. In living mammalian cells, the nonfluorescent fragments complemented and rapidly became fluorescent upon rapamycin-induced FKBP and Frb protein interaction, and lost fluorescence when the protein interaction was inhibited. This reversible fluorogenic reporter, named uPPI [UnaG-based protein-protein interaction (PPI) reporter], uses bilirubin (BR) as the chromophore and requires no exogenous cofactor. BR is an endogenous molecule in mammalian cells and is not fluorescent by itself. uPPI may have many potential applications in visualizing spatiotemporal dynamics of PPIs.

Severe obesity prior to diagnosis limits survival in colorectal cancer patients evaluated at a large cancer centre

Background:

In contrast to the consistent evidence for obesity and colorectal cancer (CRC) risk, the impact of obesity in CRC patients is less clear. In a well-characterised cohort of CRC patients, we prospectively evaluated class I and class II obesity with survival outcomes.

Methods:

The CRC patients (N=634) were followed from the date of diagnosis until disease progression/first recurrence (progression-free survival (PFS)) or death (overall survival (OS)). Body mass index (BMI) was calculated from reported usual weight prior to diagnosis. Hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated in models adjusted for clinicopathologic, treatment, and lifestyle factors.

Results:

Over a median follow-up of 4 years, 208 (33%) patients died and 235 (37%) recurred or progressed. Class II obesity, as compared with either overweight or normal weight, was associated with an increased risk of death (HR and 95% CI: 1.55 (0.97–2.48) and 1.65 (1.02–2.68), respectively), but no clear association was observed with PFS. In analyses restricted to patients who presented as stages I–III, who reported stable weight, or who were aged <50 years, obesity was associated with a significant two- to five-fold increased risk of death.

Conclusions:

In CRC patients evaluated at a large cancer centre, severely obese patients experienced worse survival outcomes independent of many other factors.

Adult patients with respiratory syncytial virus infection: impact of solid organ and hematopoietic stem cell transplantation on outcomes

BACKGROUND

Respiratory syncytial virus (RSV) is a common community-acquired pathogen responsible for a substantial disease burden in adults. We investigated the outcomes after RSV infection in hospitalized adults over a 3-year period.

METHODS

This single-center, retrospective study identified 174 patients hospitalized with RSV upper or lower respiratory tract infection (LRTI) between January 1, 2009 and June 30, 2012. Clinical data were extracted from medical records. The primary outcome analyzed was all-cause mortality, defined as death during the index hospital admission. Subjects were divided into 3 groups for comparison: hematopoietic stem cell transplant (HSCT) patients, solid organ transplant (SOT) patients, and non-transplant patients.

RESULTS

In our study, 41/174 (23.6%) were HSCT recipients and 28/174 (16.1%) were SOT recipients. Twelve of 174 (6.9%) died. Death occurred in 2/41 (4.9%) HSCT and 3/28 (10.7%) SOT recipients, compared to 7/106 (6.6%) non-transplant patients. When compared to the non-transplant cohort, HSCT and SOT were not found to be significant risk factors for mortality (P = 0.685 and 0.645, respectively). In multivariate logistic regression, age >60 was associated with mortality (P = 0.019), while lymphopenia on admission trended toward an association with death (P = 0.054). HSCT patients were less likely to be admitted to an intensive care unit (odds ratio [OR] 0.26, P = 0.04), but were significantly more likely to receive ribavirin therapy (OR 11.62, P < 0.0001).

CONCLUSION

Adults hospitalized with RSV LRTI are at significant risk of mortality, and this risk may be increased in patients age >60 or with lymphopenia on admission. This study did not identify any significant increased mortality or morbidity associated with RSV infection in immune suppressed transplant recipients vs. patients who had not received a transplant.

A naturally monomeric infrared fluorescent protein for protein labeling in vivo

Infrared fluorescent proteins (IFPs) provide an additional color to GFP and its red homologs in protein labeling. Based on structural analysis of the dimer interface, a monomeric bateriophytochrome is identified from a sequence database, and is engineered into a naturally-monomeric IFP (mIFP). We demonstrate that mIFP correctly labels proteins in live Drosophila and zebrafish requiring no exogenous cofactor, and will thus be useful in molecular, cell and developmental biology.

Enhanced formation and impaired degradation of neutrophil extracellular traps in dermatomyositis and polymyositis: a potential contributor to interstitial lung disease complications

Dermatomyositis (DM) and polymyosits (PM) are systemic autoimmune diseases whose pathogeneses remain unclear. Neutrophil extracellular traps (NETs) are reputed to play an important role in the pathogenesis of autoimmune diseases. This study tests the hypothesis that NETs may be pathogenic in DM/PM. Plasma samples from 97 DM/PM patients (72 DM, 25 PM) and 54 healthy controls were tested for the capacities to induce and degrade NETs. Plasma DNase I activity was tested to further explore possible reasons for the incomplete degradation of NETs. Results from 35 DM patients and seven PM patients with interstitial lung disease (ILD) were compared with results from DM/PM patients without ILD. Compared with control subjects, DM/PM patients exhibited a significantly enhanced capacity for inducing NETs, which was supported by elevated levels of plasma LL-37 and circulating cell-free DNA (cfDNA) in DM/PM. NETs degradation and DNase I activity were also decreased significantly in DM/PM patients and were correlated positively. Moreover, DM/PM patients with ILD exhibited the lowest NETs degradation in vitro due to the decrease in DNase I activity. DNase I activity in patients with anti-Jo-1 antibodies was significantly lower than in patients without. Glucocorticoid therapy seems to improve DNase I activity. Our findings demonstrate that excessively formed NETs cannot be degraded completely because of decreased DNase I activity in DM/PM patients, especially in patients with ILD, suggesting that abnormal regulation of NETs may be involved in the pathogenesis of DM/PM and could be one of the factors that initiate and aggravate ILD.

Singlet oxygen triplet energy transfer-based imaging technology for mapping protein-protein proximity in intact cells

Many cellular processes are carried out by large protein complexes that can span several tens of nanometres. Whereas forster resonance energy transfer has a detection range of <10 nm, here we report the theoretical development and experimental demonstration of a new fluorescence-imaging technology with a detection range of up to several tens of nanometres: singlet oxygen triplet energy transfer. We demonstrate that our method confirms the topology of a large protein complex in intact cells, which spans from the endoplasmic reticulum to the outer mitochondrial membrane and the matrix. This new method is thus suited for mapping protein proximity in large protein complexes.

An improved monomeric infrared fluorescent protein for neuronal and tumour brain imaging

Infrared fluorescent proteins (IFPs) are ideal for in vivo imaging, and monomeric versions of these proteins can be advantageous as protein tags or for sensor development. In contrast to GFP, which requires only molecular oxygen for chromophore maturation, phytochrome-derived IFPs incorporate biliverdin (BV) as the chromophore. However, BV varies in concentration in different cells and organisms. Here we engineered cells to express the haeme oxygenase responsible for BV biosynthesis and a brighter monomeric IFP mutant (IFP2.0). Together, these tools improve the imaging capabilities of IFP2.0 compared with monomeric IFP1.4 and dimeric iRFP. By targeting IFP2.0 to the plasma membrane, we demonstrate robust labelling of neuronal processes in Drosophila larvae. We also show that this strategy improves the sensitivity when imaging brain tumours in whole mice. Our work shows promise in the application of IFPs for protein labelling and in vivo imaging.

Atopic conditions and brain tumor risk in children and adolescents--an international case-control study (CEFALO)

BACKGROUND

A number of epidemiological studies indicate an inverse association between atopy and brain tumors in adults, particularly gliomas. We investigated the association between atopic disorders and intracranial brain tumors in children and adolescents, using international collaborative CEFALO data.

PATIENTS AND METHODS

CEFALO is a population-based case-control study conducted in Denmark, Norway, Sweden, and Switzerland, including all children and adolescents in the age range 7-19 years diagnosed with a primary brain tumor between 2004 and 2008. Two controls per case were randomly selected from population registers matched on age, sex, and geographic region. Information about atopic conditions and potential confounders was collected through personal interviews.

RESULTS

In total, 352 cases (83%) and 646 controls (71%) participated in the study. For all brain tumors combined, there was no association between ever having had an atopic disorder and brain tumor risk [odds ratio 1.03; 95% confidence interval (CI) 0.70-1.34]. The OR was 0.76 (95% CI 0.53-1.11) for a current atopic condition (in the year before diagnosis) and 1.22 (95% CI 0.86-1.74) for an atopic condition in the past. Similar results were observed for glioma.

CONCLUSIONS

There was no association between atopic conditions and risk of all brain tumors combined or of glioma in particular. Stratification on current or past atopic conditions suggested the possibility of reverse causality, but may also the result of random variation because of small numbers in subgroups. In addition, an ongoing tumor treatment may affect the manifestation of atopic conditions, which could possibly affect recall when reporting about a history of atopic diseases. Only a few studies on atopic conditions and pediatric brain tumors are currently available, and the evidence is conflicting.

Aggregate human health risk assessment from dust of daily life in the urban environment of Beijing

Because of the high emissions of polycyclic aromatic hydrocarbons (PAHs) into the environment by the increasing number of vehicles in Beijing and the absorption of these PAHs onto particulates, the performance of a preliminary health risk assessment of the aggregate exposure to PAHs of urban citizens in daily life is very important. Urban dust can be used to examine the aggregation of atmospheric particulates from local pollution sources over a long time period and the direct exposure of the urban human population. The environment's correlative with clothing, dining, residing, and traveling in urban daily life was assessed using exposure-receptor-oriented analysis. The multipathway exposure model was used to simulate the lifetime exposure of a female citizen to PAHs in dust. All of the PAH concentrations in dust for each behavior and its correlative environment in Beijing were acceptable because all of the carcinogenic risks of PAHs in the dust were approximately 1.0 × 10(-6). The dominant induced carcinogenic risks in the dust were Benzo(a)pyrene and Dibenzo(a,h)anthracene. The main carcinogenic risk routes for humans were dermal contact and oral intake, which contributed on average 99.78% of the risk. Indoor risk is especially important, as the decoration and height within the building were important impact factors for carcinogenic risk induced by indoor PAHs. For people living in an urban area, a healthy lifestyle includes less decoration per room, living on a low floor, wearing a respirator, and reducing exposed skin area when traveling.

Protein kinase B phosphorylation correlates with vascular endothelial growth factor A and microvessel density in gastric adenocarcinoma

OBJECTIVE

The signalling molecule protein kinase B (Akt) modulates many cellular processes. Phosphatidylinositol 3-kinase (PI3K)/Akt signalling pathways play important roles in tumour angiogenesis. The aim of this study was to determine the role of phosphorylated Akt (pAkt) in angiogenesis and its correlation with vascular endothelial growth factor (VEGF)-A in gastric adenocarcinoma.

METHODS

Tumour tissue and matched healthy gastric mucosa were obtained from patients undergoing surgical resection of gastric adenocarcinoma. Akt and pAkt were detected via Western blotting. VEGF-A, pAkt and CD34 were examined by immunohistochemistry.

RESULTS

Akt and pAkt protein levels were significantly higher in gastric cancer tissue than in normal tissue (n = 48 patients). Positive VEGF-A immunostaining was significantly associated with pAkt immunostaining. Microvessel density was correlated with both VEGF-A and pAkt positivity.

CONCLUSIONS

Phosphorylated Akt and VEGF-A are involved in angiogenesis of gastric adenocarcinoma, and Akt activation may contribute to angiogenesis via VEGF-A upregulation. The PI3K/Akt/VEGF signalling pathway may be involved in gastric adeno carcinoma.

A structural basis for the assembly and functions of a viral polymer that inactivates multiple tumor suppressors

Evolution of minimal DNA tumor virus' genomes has selected for small viral oncoproteins that hijack critical cellular protein interaction networks. The structural basis for the multiple and dominant functions of adenovirus oncoproteins has remained elusive. E4-ORF3 forms a nuclear polymer and simultaneously inactivates p53, PML, TRIM24, and MRE11/RAD50/NBS1 (MRN) tumor suppressors. We identify oligomerization mutants and solve the crystal structure of E4-ORF3. E4-ORF3 forms a dimer with a central β core, and its structure is unrelated to known polymers or oncogenes. E4-ORF3 dimer units coassemble through reciprocal and nonreciprocal exchanges of their C-terminal tails. This results in linear and branched oligomer chains that further assemble in variable arrangements to form a polymer network that partitions the nuclear volume. E4-ORF3 assembly creates avidity-driven interactions with PML and an emergent MRN binding interface. This reveals an elegant structural solution whereby a small protein forms a multivalent matrix that traps disparate tumor suppressors.

Vascular smooth muscle cell apoptosis promotes transplant arteriosclerosis through inducing the production of SDF-1α

Transplant arteriosclerosis is a leading cause of late allograft loss. Medial smooth muscle cell (SMC) apoptosis is considered to be an important event in transplant arteriosclerosis. However, the precise contribution of medial SMC apoptosis to transplant arteriosclerosis and the underlying mechanisms remain unclear. We transferred wild-type p53 to induce apoptosis of cultured SMCs. We found that apoptosis induces the production of SDF-1α from apoptotic and neighboring viable cells, resulting in increased SDF-1α in the culture media. Conditioned media from Ltv-p53-transferred SMCs activated PI3K/Akt/mTOR and MAPK/Erk signaling in a SDF-1α-dependent manner and thereby promoted mesenchymal stem cell (MSC) migration and proliferation. In a rat aorta transplantation model, lentivirus-mediated BclxL transfer selectively inhibits medial SMC apoptosis in aortic allografts, resulting in a remarkable decrease of SDF-1α both in allograft media and in blood plasma, associated with diminished recruitment of CD90(+)CD105(+) double-positive cells and impaired neointimal formation. Systemic administration of rapamycin or PD98059 also attenuated MSC recruitment and neointimal formation in the aortic allografts. These results suggest that medial SMC apoptosis is critical for the development of transplant arteriosclerosis through inducing SDF-1α production and that MSC recruitment represents a major component of vascular remodeling, constituting a relevant target and mechanism for therapeutic interventions.

Association of genetic variation in FTO with risk of obesity and type 2 diabetes with data from 96,551 East and South Asians

AIMS/HYPOTHESIS

FTO harbours the strongest known obesity-susceptibility locus in Europeans. While there is growing evidence for a role for FTO in obesity risk in Asians, its association with type 2 diabetes, independently of BMI, remains inconsistent. To test whether there is an association of the FTO locus with obesity and type 2 diabetes, we conducted a meta-analysis of 32 populations including 96,551 East and South Asians.

METHODS

All studies published on the association between FTO-rs9939609 (or proxy [r (2) > 0.98]) and BMI, obesity or type 2 diabetes in East or South Asians were invited. Each study group analysed their data according to a standardised analysis plan. Association with type 2 diabetes was also adjusted for BMI. Random-effects meta-analyses were performed to pool all effect sizes.

RESULTS

The FTO-rs9939609 minor allele increased risk of obesity by 1.25-fold/allele (p = 9.0 × 10(-19)), overweight by 1.13-fold/allele (p = 1.0 × 10(-11)) and type 2 diabetes by 1.15-fold/allele (p = 5.5 × 10(-8)). The association with type 2 diabetes was attenuated after adjustment for BMI (OR 1.10-fold/allele, p = 6.6 × 10(-5)). The FTO-rs9939609 minor allele increased BMI by 0.26 kg/m(2) per allele (p = 2.8 × 10(-17)), WHR by 0.003/allele (p = 1.2 × 10(-6)), and body fat percentage by 0.31%/allele (p = 0.0005). Associations were similar using dominant models. While the minor allele is less common in East Asians (12-20%) than South Asians (30-33%), the effect of FTO variation on obesity-related traits and type 2 diabetes was similar in the two populations.

CONCLUSIONS/INTERPRETATION

FTO is associated with increased risk of obesity and type 2 diabetes, with effect sizes similar in East and South Asians and similar to those observed in Europeans. Furthermore, FTO is also associated with type 2 diabetes independently of BMI.

Subsequent cancers in patients diagnosed with cancer of unknown primary (CUP): etiological insights?

BACKGROUND

Patterns of subsequent malignancies in patients with cancer of unknown primary (CUP) may provide etiological insight into the primary tumor. The objective of the present study is to quantify risks of the subsequent cancers in CUP patients since such studies are lacking.

PATIENTS AND METHODS

A population-based cohort of CUP was identified from the Swedish Family-Cancer Database of year 2008. Standardized incidence ratios (SIRs) were calculated for developing the following malignancies in 31,357 CUP patients from 1975 to 2008.

RESULTS

A total of 755 CUP patients developed subsequent cancers, showing a significantly increased overall SIR of 1.69 (95% confidence interval 1.57-1.81). Among the most common 32 malignancies, increased SIRs were noted for 16 sites. Over 10-fold increases were observed for squamous cell carcinoma at four sites, possibly as a result of uncontrolled human papillomavirus infection due to faltering immune surveillance. The highest SIRs were observed among CUP patients diagnosed at a younger age and during the first follow-up year.

CONCLUSIONS

Swedish CUP survivors had a higher risk of developing many subsequent cancers. Different patterns of risk excess may be suggestive of possible roles for disease- and therapy-related immunosuppression, reappearance of hidden primary tumors, or genetic predisposition.

Picking faces out of a crowd: genetic labels for identification of proteins in correlated light and electron microscopy imaging

Correlated light and electron microscopic (CLEM) imaging is a powerful method for dissecting cell and tissue function at high resolution. Each imaging mode provides unique information, and the combination of the two can contribute to a better understanding of the spatiotemporal patterns of protein expression, trafficking, and function. Critical to these methods is the use of genetically appended tags that highlight specific proteins of interest in order to be able to pick them out of their complex cellular environment. Here we review and discuss the current generation of genetic labels for direct protein identification by CLEM, addressing their relative strengths and weaknesses and in what experiments they would be most useful.

Implications of QRS duration in dogs with pacing-induced heart failure

The objective of this study was to find out the implication of QRS duration in dogs with rapid pacing-induced heart failure. Sixteen Beagle dogs were implanted with transvenous cardiac pacemakers and underwent rapid right ventricular pacing for 3 weeks at 260 bpm to induce heart failure. Dogs were divided into two groups according to the QRS duration: 9 with normal QRS duration (<100 ms) and 7 with prolonged QRS duration (≥100 ms). Cardiac systolic function and size was analyzed by real time 3-dimensional echocardiography and left ventricular dyssynchrony was assessed by speckle tracking strain imaging. Congestive heart failure developed 3 weeks after rapid right ventricular pacing. Dogs with prolonged QRS duration showed more extensive radial strain and circumferential strain dyssynchrony than dogs with normal QRS duration. At the end of 4-week recovery, greater improvement of left ventricular ejection fraction and left ventricular end-systolic volume was detected in dogs with normal QRS duration. The findings suggested that left ventricular dyssynchrony, indicated by a prolonged QRS duration, predicted an unsatisfying recovery in dogs with rapid pacing-induced heart failure. QRS duration had the potential to be a prognostic indicator for dogs with heart failure.

Spiers Memorial Lecture. Breeding and building molecular spies

To circumvent the limited spatial resolution of fluorescent protein imaging, we are developing genetically encoded tags for electron microscopy (EM).

A genetically encoded tag for correlated light and electron microscopy of intact cells, tissues, and organisms

Electron microscopy (EM) achieves the highest spatial resolution in protein localization, but specific protein EM labeling has lacked generally applicable genetically encoded tags for in situ visualization in cells and tissues. Here we introduce “miniSOG” (for mini Singlet Oxygen Generator), a fluorescent flavoprotein engineered from Arabidopsis phototropin 2. MiniSOG contains 106 amino acids, less than half the size of Green Fluorescent Protein. Illumination of miniSOG generates sufficient singlet oxygen to locally catalyze the polymerization of diaminobenzidine into an osmiophilic reaction product resolvable by EM. MiniSOG fusions to many well-characterized proteins localize correctly in mammalian cells, intact nematodes, and rodents, enabling correlated fluorescence and EM from large volumes of tissue after strong aldehyde fixation, without the need for exogenous ligands, probes, or destructive permeabilizing detergents. MiniSOG permits high quality ultrastructural preservation and 3-dimensional protein localization via electron tomography or serial section block face scanning electron microscopy. EM shows that miniSOG-tagged SynCAM1 is presynaptic in cultured cortical neurons, whereas miniSOG-tagged SynCAM2 is postsynaptic in culture and in intact mice. Thus SynCAM1 and SynCAM2 could be heterophilic partners. MiniSOG may do for EM what Green Fluorescent Protein did for fluorescence microscopy.

Electron microscopy (EM) once revolutionized cell biology by revealing subcellular anatomy at resolutions of tens of nanometers, well below the diffraction limit of light microscopy. Over the past two decades, light microscopy has been revitalized by the development of spontaneously fluorescent proteins, which allow nearly any protein of interest to be specifically tagged by genetic fusion. EM has lacked comparable genetic tags that are generally applicable. Here, we introduce “miniSOG”, a small (106-residue) fluorescent flavoprotein that efficiently generates singlet oxygen when illuminated by blue light. In fixed tissue, photogenerated singlet oxygen locally polymerizes diaminobenzidine into a precipitate that is stainable with osmium and therefore can be readily imaged at high resolution by EM. Thus miniSOG is a versatile label for correlated light and electron microscopy of genetically tagged proteins in cells, tissues, and organisms including intact nematodes and mice. As a demonstration of miniSOG's capabilities, controversies about the localization of synaptic cell adhesion molecules are resolved by EM of miniSOG fusions in neuronal culture and intact mouse brain.

Inflammatory pseudotumoural endotracheal mucormycosis with cartilage damage

Mucormycosis is a rare opportunistic infection usually associated with immunosuppression, diabetes mellitus or haematological malignancy. Herein, we report an unusual case of mucormycosis in a 46-yr-old male patient with diabetes presenting with an endotracheal mass obstructing the trachea and cartilage damage. Histological examination of the bronchoscopy biopsy specimens revealed invasive mucormycosis. The patient was treated with intravenous amphotericin B followed by removal of the lesion via bronchoscopy.

Cancer risk among patients hospitalized for Type 1 diabetes mellitus: a population-based cohort study in Sweden

AIMS

Type 1 diabetes mellitus (T1DM) is an autoimmune disease with potential mechanistic links to immune-related cancers. We aimed at examining the overall and specific cancer risks among hospitalized T1DM patients from the national registers in Sweden.

METHODS

A T1DM research cohort was created by identifying T1DM patients from the Hospital Discharge Register and linking them with the Cancer Registry. Standardized incidence ratios (SIRs) for subsequent cancers were calculated among patients with T1DM compared with those without T1DM.

RESULTS

Two hundred and fifty-eight cases were ascertained with subsequent cancers during the follow-up duration from 1964 to 2006, with an increased overall SIR of 1.17 (95% CI 1.04-1.33) among 24 052 T1DM patients identified at baseline. Significant excess was noted for gastric and skin (squamous cell carcinoma) cancers and for leukaemia. Increased risk of acute lymphatic leukaemia accounted for most of the variation of leukaemia risk (SIR = 5.31, 95% CI 3.32-8.05). Cancer risk varied with sex, age at first hospitalization and numbers of hospitalizations. The risk was higher in women compared with men and in those hospitalized for T1DM at age over 10 years compared with the younger patients. Higher risks were also found among those with more hospital visits.

CONCLUSION

By quantifying the variations of overall and site-specific cancer risks after T1DM, the current study provides novel associations between T1DM and subsequent cancers, the mechanisms of which remain to be established.

Unique interactions between the chromophore and glutamate 16 lead to far-red emission in a red fluorescent protein

mPlum is a far-red fluorescent protein with emission maximum at approximately 650 nm and was derived by directed evolution from DsRed. Two residues near the chromophore, Glu16 and Ile65, were previously revealed to be indispensable for the far-red emission. Ultrafast time-resolved fluorescence emission studies revealed a time dependent shift in the emission maximum, initially about 625 nm, to about 650 nm over a period of 500 ps. This observation was attributed to rapid reorganization of the residues solvating the chromophore within mPlum. Here, the crystal structure of mPlum is described and compared with those of two blue shifted mutants mPlum-E16Q and -I65L. The results suggest that both the identity and precise orientation of residue 16, which forms a unique hydrogen bond with the chromophore, are required for far-red emission. Both the far-red emission and the time dependent shift in emission maximum are proposed to result from the interaction between the chromophore and Glu16. Our findings suggest that significant red shifts might be achieved in other fluorescent proteins using the strategy that led to the discovery of mPlum.

Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome

Visibly fluorescent proteins (FPs) from jellyfish and corals have revolutionized many areas of molecular and cell biology, but the use of FPs in intact animals, such as mice, has been handicapped by poor penetration of excitation light. We now show that a bacteriophytochrome from Deinococcus radiodurans, incorporating biliverdin as the chromophore, can be engineered into monomeric, infrared-fluorescent proteins (IFPs), with excitation and emission maxima of 684 and 708 nm, respectively; extinction coefficient >90,000 M(-1) cm(-1); and quantum yield of 0.07. IFPs express well in mammalian cells and mice and spontaneously incorporate biliverdin, which is ubiquitous as the initial intermediate in heme catabolism but has negligible fluorescence by itself. Because their wavelengths penetrate tissue well, IFPs are suitable for whole-body imaging. The IFPs developed here provide a scaffold for further engineering.

Cancer risk in hospitalised asthma patients

Asthma is an increasingly common disorder, affecting 5–10% of the population. It involves a dysregulated immune function, which may predispose to subsequent cancer. We examined cancer risk among Swedish subjects who had hospital admission once or multiple times for asthma. An asthma research database was created by identifying asthma patients from the Swedish Hospital Discharge Register and by linking them with the Cancer Registry. A total of 140 425 patients were hospitalised for asthma during 1965–2004, of whom 7421 patients developed cancer, giving an overall standardised incidence ratio (SIR) of 1.36. A significant increase was noted for most sites, with the exception of breast and ovarian cancers and non-Hodgkin's lymphoma and myeloma. Patients with multiple hospital admissions showed a high risk, particularly for stomach (SIR 1.70) and colon (SIR 1.99) cancers. A significant decrease was noted for endometrial cancer and skin melanoma. Oesophageal and lung cancers showed high risks throughout the study period, whereas stomach cancer increased towards the end of the period. The relatively stable temporal trends suggest that the asthmatic condition rather than its medication is responsible for the observed associations.

Effect of Helicobacter pylori eradication on oncogenes and cell proliferation

BACKGROUND

Helicobacter pylori , the main cause of chronic gastritis, is a class 1 gastric carcinogen. However, it remains unclear whether H. pylori affects molecular alterations in chronic gastritis. Thus, this study was designed to investigate the effect of H. pylori eradication on the expression of human telomerase RNA (hTR), human telomerase reverse transcriptase (hTERT), c-myc and proliferation nuclear cell antigen (PCNA) in H. pylori associated chronic gastritis.

MATERIALS AND METHODS

hTR was determined by in situ hybridization, hTERT, c-myc and PCNA were detected by immunohistochemistry using stomach tissues obtained from 39 H. pylori-infected and 21 H. pylori-negative patients with chronic gastritis before and after H. pylori eradication therapy or treatment for symptom relief only.

RESULTS

Levels of hTR, hTERT, c-myc and PCNA were significantly higher in H. pylori-infected mucosa (51.3%, 53.8%, 53.8% and 16.8 +/- 5.8, respectively) when compared to H. pylori-negative mucosa before therapy (19.0%, 23.8%, 28.6%, 8.8 +/- 3.4, respectively; P < 0.05 in all cases). In patients with successful eradication of H. pylori the levels of hTR, hTERT, c-myc and PCNA (55.5%, 59.3%, 59.3%, 16.8 +/- 5.8, respectively) were significantly reduced after the therapy (22.2%, 22.2%, 14.8%, 7.0 +/- 5.0, respectively; P < 0.05 in all cases). In the H. pylori failed eradication and H. pylori-negative groups, there was no statistical difference in all four measurements.

CONCLUSIONS

H. pylori infection may induce the overexpression of hTR, hTERT, c-myc and stimulate cell proliferation. Eradication of H. pylori may reverse the aberrant expression of these oncoproteins and thus correct the abnormal cell proliferation.

Ultrafast excited-state dynamics in the green fluorescent protein variant S65T/H148D. 1. Mutagenesis and structural studies

Wild type green fluorescent protein (wt-GFP) and the variant S65T/H148D each exhibit two absorption bands, A and B, which are associated with the protonated and deprotonated chromophores, respectively. Excitation of either band leads to green emission. In wt-GFP, excitation of band A ( approximately 395 nm) leads to green emission with a rise time of 10-15 ps, due to excited-state proton transfer (ESPT) from the chromophore hydroxyl group to an acceptor. This process produces an anionic excited-state intermediate I* that subsequently emits a green photon. In the variant S65T/H148D, the A band absorbance maximum is red-shifted to approximately 415 nm, and as detailed in the accompanying papers, when the A band is excited, green fluorescence appears with a rise time shorter than the instrument time resolution ( approximately 170 fs). On the basis of the steady-state spectroscopy and high-resolution crystal structures of several variants described herein, it is proposed that in S65T/H148D, the red shift of absorption band A and the ultrafast appearance of green fluorescence upon excitation of band A are due to a very short ( Collapse

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MESH Headings

• Green Fluorescent Proteins/chemistry
• Green Fluorescent Proteins/genetics
• Models, Molecular
• Mutagenesis
• Protein Conformation
• Spectrophotometry, Ultraviolet

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Grants

• R37 GM027738-22S1 NIGMS NIH HHS
• R01 GM042618-12S1 NIGMS NIH HHS
• R37 GM027738-20 NIGMS NIH HHS
• R01 GM042618-12 NIGMS NIH HHS
• R01 GM027738 NIGMS NIH HHS
• R01 GM042618-11 NIGMS NIH HHS
• R01 GM42618 NIGMS NIH HHS
• R01 GM042618 NIGMS NIH HHS
• R37 GM027738 NIGMS NIH HHS
• R37 GM027738-22 NIGMS NIH HHS
• R01 GM042618-08 NIGMS NIH HHS
• R37 GM027738-23 NIGMS NIH HHS
• R01 GM042618-14 NIGMS NIH HHS
• GM 27738 NIGMS NIH HHS
• R01 GM042618-13A1 NIGMS NIH HHS
• R01 GM042618-10 NIGMS NIH HHS
• R37 GM027738-21 NIGMS NIH HHS
• R01 GM042618-09 NIGMS NIH HHS

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Ultrafast excited-state dynamics in the green fluorescent protein variant S65T/H148D. 2. Unusual photophysical properties

In the preceding accompanying paper [Shu, X., et al. (2007) Biochemistry 46, 12005-12013], the 1.5 A resolution crystal structure of green fluorescent protein (GFP) variant S65T/H148D is presented, and the possible consequences of an unusual short hydrogen bond ( Collapse

Key Words Collapse

MESH Headings

• Green Fluorescent Proteins/chemistry
• Kinetics
• Photochemistry
• Physical Phenomena
• Physics
• Spectrometry, Fluorescence

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Grants

• R01 GM042618 NIGMS NIH HHS
• R37 GM027738 NIGMS NIH HHS
• GM27738 NIGMS NIH HHS
• R01 GM027738-25 NIGMS NIH HHS
• R01 GM027738-28 NIGMS NIH HHS
• R01 GM027738 NIGMS NIH HHS
• R01 GM027738-27 NIGMS NIH HHS
• R01GM42618 NIGMS NIH HHS
• R01 GM027738-26 NIGMS NIH HHS

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An alternative excited-state proton transfer pathway in green fluorescent protein variant S205V

Wild-type green fluorescent protein (wt-GFP) has a prominent absorbance band centered at approximately 395 nm, attributed to the neutral chromophore form. The green emission arising upon excitation of this band results from excited-state proton transfer (ESPT) from the chromophore hydroxyl, through a hydrogen-bond network proposed to consist of a water molecule and Ser205, to Glu222. Although evidence for Glu222 as a terminal proton acceptor has already been obtained, no evidence for the participation of Ser205 in the proton transfer process exists. To examine the role of Ser205 in the proton transfer, we mutated Ser205 to valine. However, the derived GFP variant S205V, upon excitation at 400 nm, still produces green fluorescence. Time-resolved emission spectroscopy suggests that ESPT contributes to the green fluorescence, and that the proton transfer takes place approximately 30 times more slowly than in wt-GFP. The crystal structure of S205V reveals rearrangement of Glu222 and Thr203, forming a new hydrogen-bonding network. We propose this network to be an alternative ESPT pathway with distinctive features that explain the significantly slowed rate of proton transfer. In support of this proposal, the double mutant S205V/T203V is shown to be a novel blue fluorescent protein containing a tyrosine-based chromophore, yet is incapable of ESPT. The results have implications for the detailed mechanism of ESPT and the photocycle of wt-GFP, in particular for the structures of spectroscopically identified intermediates in the cycle.

Influence of UGT1A9 intronic I399C>T polymorphism on SN-38 glucuronidation in Asian cancer patients

Genetic polymorphisms in hepatically expressed UGT1A1 and UGT1A9 contribute to the interindividual variability i-n irinotecan disposition and toxicity. We screened UGT1A1 (UGT1A1*60, g.-3140G>A, UGT1A1*28 and UGT1A1*6) and UGT1A9 (g.-118(T)(9>10) and I399C>T) genes for polymorphic variants in the promoter and coding regions, and the genotypic effect of UGT1A9 I399C>T polymorphism on irinotecan disposition in Asian cancer patients was investigated. Blood samples were collected from 45 patients after administration of irinotecan as a 90 min intravenous infusion of 375 mg/m(2) once in every 3 weeks. Genotypic-phenotypic correlates showed that cancer patients heterozygous or homozygous for the I399C>T allele had approximately 2-fold lower systemic exposure to SN-38 (P<0.05) and a trend towards a higher relative extent of glucuronidation (REG) of SN-38 (P>0.05). UGT1A1-1A9 diplotype analysis showed that patients harbouring the H1/H2 (TG6GT(10)T/GG6GT(9)C) diplotype had 2.4-fold lower systemic exposure to SN-38 glucuronide (SN-38G) compared with patients harbouring the H1/H5 (TG6GT(10)T/GG6GT(10)C) diplotype (P=0.025). In conclusion, this in vivo study supports the in vitro findings of Girard et al. and suggests that the UGT1A9 I399C>T variant may be an important glucuronidating allele affecting the pharmacokinetics of SN-38 and SN-38G in Asian cancer patients receiving irinotecan chemotherapy.

Hepatic expression of UGT enzymes and implications in pharmacokinetic variations in Asians during chemotherapy

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Background: The objective of this study was to screen the promoter and relevant coding regions in the UGT1A1 and UGT1A9 genes and genotypically quantitate expression of these genes in hepatic tissues obtained from Asian cancer patients undergoing hepatectomy. Methods: Non-cancerous Asian hepatic tissues (Chinese: N=36; Malay: N=1; Indian: N=3) were obtained from the institution’s central tissue repository bank. Messenger RNA was isolated from each tissue sample and reverse transcribed to cDNA followed by real time PCR experiments. Results from these gene expression experiments were normalized against GAPDH transcripts. DNA was also extracted from the hepatocytes, screened for variations in the promoter regions (UGT1A1*60, g.3140G>A and UGT1A1*28) and exon 1 (UGT1A1*6) of the UGT1A1 and UGT1A9 (UGT1A9*22, I399C>T) genes. Results: Large interindividual variations were observed in the hepatic expression pattern of UGT1A1 and UGT1A9 mRNA with respect to the different polymorphic variants. There was no significant association between hepatic expression of UGT1A1 mRNA and UGT1A1*60, g-3140G>A and *6 genotypes (P>0.05 in each case). The median expression level of UGT1A1 mRNA was approximately 2-fold higher in liver tissues harboring UGT1A1 6/6 (reference) genotype (N=27, median = 0.478; range: 0.065 to 3.125) compared to the heterozygous 6/7 genotype (N=9, median = 0.254; range: 0.042 to 1.894; P=0.77). The median expression levels of UGT1A9 mRNA were approximately 3-fold higher in liver tissues harboring I399CC genotype (N=3, median = 2.735; range: 0.702 to 3.375) when compared with the homozygous variant TT genotype (N=8, median = 0.973; range: 0.652 to 4.155; P=0.88). Conclusions: The results showed that polymorphisms in the UGT1A genes may influence the expression pattern of the respective proteins and could contribute to the high degree of interpatient variability in the glucuronidation dependent metabolism and elimination of chemotherapeutic agents in Asian cancer patients.

No significant financial relationships to disclose.

All-optical demultiplexing of 640 to 40 Gbits/s using filtered chirp of a semiconductor optical amplifier

We present a high-capacity ultrafast all-optical time demultiplexer that can be employed to retrieve 40 gigabits/second (Gb/s) base-rate channels from a 640 Gb/s single-polarized signal. The demultiplexer utilizes ultrafast effects of filtered chirp of a semiconductor optical amplifier. Excellent demultiplexing performance is shown at very low switching powers: +8 dBm (640 Gb/s data) and -14 dBm (40 GHz clock). The demultiplexer has a simple structure and, in principle, allows monolithic integration.